Project Outline

Few diseases have had a more significant impact on human health than tuberculosis. This on-going pandemic claims 1.6 million lives annually and is the 13th leading cause of death world-wide according to the WHO. The biology of tuberculosis is marked by a complex and multi-stage inflammatory process driven by Mycobacterium tuberculosis. The cell envelope of these bacteria acts as the major interface between the host and pathogen. This structure is dominated by a macromolecule comprised of mycolic acids, arabinogalactan, and peptidoglycan with many intercalated lipids such as lipoarabinomannan (LAM). These molecules, or fragments of them, serve as important signals to the host, driving complex interactions at once provoking and inhibiting inflammatory responses. What is less well understood is that fragments of these structures also serve as important signals for the bacteria. In this project the student will take advantage of our recent discovery of new cell wall degrading enzymes and use omics-methods such as RNAseq and proteomics to identify the regulatory pathways driven by the action of these enzymes. The student will gain experience in biochemistry, microbiology, proteomics, RNAseq and the bioinformatic tools required for the analysis of their data. They can also engage in structural biology and molecular microbiology, as the needs of the project or their personal interest require..

Techniques

My laboratory employs a wide range of techniques to answer fundamental questions about bacterial biology (see: https://www.nature.com/articles/s41467-019-10586-2; https://www.nature.com/articles/s41467-023-37839-5). In this project the student will tackle their research question from two main directions. First, they will gain experience cultivating mycobacteria and optimising phenotypic responses to cell wall metabolites, some of which we have already preliminarily established. This will involve working with high-throughput robotics and biochemical techniques. The student will then investigate these phenotypes through approaches such as RNASeq or proteomics. Finally the student can investigate proteins of interest through biochemistry by recombinantly producing and purifying target proteins and structural biology techniques including X-ray crystallography. The student can also investigate function through bacterial cell biology using knock-out strains of the bacteria, making use of fluorescent probes and a range of analytical techniques including mass spectrometry.